REFAC: Shift terminology from Cognitive Loop to Cognitive Cycle

README.org

@@ -41,7 +41,7 @@ To guarantee long-term stability, opencortex enforces a strict architectural bou
 The Lisp microkernel does almost no actual "work." It is a thin, unbreakable harness strictly responsible for three things:
 1. *The Memory:* Maintaining the live graph of your Memex in RAM.
 2. *The Communication Protocol:* Managing the secure bridge between the agent and the outside world. While power users can connect natively via Emacs or Vim, the vast majority of users will interact with opencortex exclusively through chat clients (like Telegram, Signal, or Matrix), web dashboards, or a Terminal UI (TUI). The harness doesn't care; it just securely routes the messages.
-3. *The Cognitive Loop:* Moving signals through the Perceive -> Probabilistic -> Deterministic -> Dispatch pipeline.
+3. *The Cognitive Cycle:* Moving signals through the Perceive -> Probabilistic -> Deterministic -> Dispatch pipeline.
 
 Everything else—AI routing, vector embeddings, shell execution, or web browsing—is pushed entirely out of the harness and into *Fat Skills*.
 

literate/setup.org

@@ -130,6 +130,31 @@ NC='\033[0m'
 
 command_exists() { command -v "$1" >/dev/null 2>&1; }
 
+update_opencortex() {
+    echo -e "${BLUE}Updating OpenCortex...${NC}"
+    if [ -d ".git" ]; then
+        echo "Pulling latest changes from repository..."
+        git pull origin main
+    fi
+    if [ -f .env ]; then
+        SKILLS_DIR=$(grep "^SKILLS_DIR=" .env | cut -d"\"" -f2)
+        SKILLS_DIR=${SKILLS_DIR:-$(pwd)/notes}
+        echo "Synchronizing core skills to $SKILLS_DIR..."
+        mkdir -p "$SKILLS_DIR"
+        cp -n skills/*.org "$SKILLS_DIR/" 2>/dev/null || true
+    fi
+    if command_exists docker-compose && [ -f "docker-compose.yml" ]; then
+        echo "Rebuilding Docker image..."
+        docker-compose up -d --build
+    fi
+    echo -e "${GREEN}✓ Update complete.${NC}"
+    exit 0
+}
+
+if [[ "$1" == "--update" ]]; then
+    update_opencortex
+fi
+
 # 1. Try to drop straight into the CLI chat
 if command_exists socat && socat - TCP:$HOST:$PORT,connect-timeout=1 2>/dev/null; then
     echo -e "${BLUE}Connected to autonomous brain at $HOST:$PORT...${NC}"
@@ -195,7 +220,7 @@ if [ -f "docker-compose.yml" ] && [ -d "literate" ]; then
         # Seed Core Skills
         echo -e "\n${BLUE}Seeding Skills...${NC}"
         MEMEX_TARGET=$(dirname $(dirname "$INSTALL_DIR"))
-        SKILLS_DIR="$MEMEX_TARGET/notes"
+        SKILLS_DIR=$(grep "^SKILLS_DIR=" .env | cut -d"\"" -f2) ; SKILLS_DIR=${SKILLS_DIR:-$MEMEX_TARGET/notes}
         mkdir -p "$SKILLS_DIR"
         cp -n skills/*.org "$SKILLS_DIR/" 2>/dev/null || true
         echo -e "${GREEN}✓ Core skills seeded to $SKILLS_DIR.${NC}"

opencortex.sh

@@ -12,6 +12,31 @@ NC='\033[0m'
 
 command_exists() { command -v "$1" >/dev/null 2>&1; }
 
+update_opencortex() {
+    echo -e "${BLUE}Updating OpenCortex...${NC}"
+    if [ -d ".git" ]; then
+        echo "Pulling latest changes from repository..."
+        git pull origin main
+    fi
+    if [ -f .env ]; then
+        SKILLS_DIR=$(grep "^SKILLS_DIR=" .env | cut -d"\"" -f2)
+        SKILLS_DIR=${SKILLS_DIR:-$(pwd)/notes}
+        echo "Synchronizing core skills to $SKILLS_DIR..."
+        mkdir -p "$SKILLS_DIR"
+        cp -n skills/*.org "$SKILLS_DIR/" 2>/dev/null || true
+    fi
+    if command_exists docker-compose && [ -f "docker-compose.yml" ]; then
+        echo "Rebuilding Docker image..."
+        docker-compose up -d --build
+    fi
+    echo -e "${GREEN}✓ Update complete.${NC}"
+    exit 0
+}
+
+if [[ "$1" == "--update" ]]; then
+    update_opencortex
+fi
+
 # 1. Try to drop straight into the CLI chat
 if command_exists socat && socat - TCP:$HOST:$PORT,connect-timeout=1 2>/dev/null; then
     echo -e "${BLUE}Connected to autonomous brain at $HOST:$PORT...${NC}"
@@ -77,7 +102,7 @@ if [ -f "docker-compose.yml" ] && [ -d "literate" ]; then
         # Seed Core Skills
         echo -e "\n${BLUE}Seeding Skills...${NC}"
         MEMEX_TARGET=$(dirname $(dirname "$INSTALL_DIR"))
-        SKILLS_DIR="$MEMEX_TARGET/notes"
+        SKILLS_DIR=$(grep "^SKILLS_DIR=" .env | cut -d"\"" -f2) ; SKILLS_DIR=${SKILLS_DIR:-$MEMEX_TARGET/notes}
         mkdir -p "$SKILLS_DIR"
         cp -n skills/*.org "$SKILLS_DIR/" 2>/dev/null || true
         echo -e "${GREEN}✓ Core skills seeded to $SKILLS_DIR.${NC}"

tests/immune-system-tests.lisp

@@ -28,8 +28,8 @@
     (clrhash opencortex::*skills-registry*)
     (setf (gethash "crasher" opencortex::*skills-registry*) skill)
     
-    ;; Since cognitive-loop is recursive and our core hooks inject a NEW stimulus,
+    ;; Since cognitive-cycle is recursive and our core hooks inject a NEW stimulus,
-    ;; we can't easily capture it in a single synchronous call without mocking cognitive-loop.
+    ;; we can't easily capture it in a single synchronous call without mocking cognitive-cycle.
     ;; However, we can check if harness-log received the "SYSTEM ERROR" message.
     (harness-log "CLEAN LOG")
     (opencortex:process-signal stimulus)